Presiding Judge Denise Cote recently refused Apple’s request to temporarily stay her decision, which would have given the company additional time to seek an appeal of the penalties laid out by the U.S. Department of Justice according to in-court reports from the Associated Press. Previously, Judge Cote found Apple guilty of colluding with HarperCollins, Hachette, Simon & Schuster, Penguin Group and Macmillan to fix the price of e-books sold through the iBookstore. The antitrust suit was leveled by the Justice Department, which ended up focusing on the company’s “agency model” agreements that allow publishers to set their own e-book prices under most favored nation’s clauses.

The DOJ submitted a proposed settlement following the ruling, which would see Apple terminate existing contracts with the five publishing houses, as well as bar any further agency model deals for five years. In addition, the Justice Department wants to bar Apple from entering similar agency arrangements with providers of “music, movies, television, shows or other content that are likely to increase the prices at which Apple’s competitors may sell that content.” Some saw this as overreaching as it would extend the proposal’s scope beyond the iBookstore and into the iTunes Store.

In a recent court filing, the publishers, all of which settled before the trial started, challenged the DOJ’s suggestion to discontinue existing agreements. They argued that such a clause would punish them more than it does Apple. The comments led the DOJ to issue a court filing where it ended up accusing Apple of banding together with the book publishers once again. Apple ended up calling the proposal a “draconian and punitive intrusion” on its iBookstore and promised to appeal Judge Cote’s ruling. This appeal could be in jeopardy with Friday’s denial.